How do I resize a folded box without messing up the folds on the top or stretching out the squares (thus messing up mapping)?
There are many ways, a simple one is:


go in edit mode (tab)
select all edges in the base of the cube (xray mode can help you to select all the base)
G (to move the selection), Z (to block the movement only in the Z axis), move mouse to decide how far to move the base of the cube




HOW TO FIX THE UV:


fix the geometry in edit mode --> the texture is now stretched





go into UV editor, select the faces with stretched texture, go into UV editor, select the base nodes (the one that you moved to change the size of the box) and move them into the UV editor to fix the textures: